The effects of biofumigation using a Brassica juncea (mustard) cover crop on the dynamics of rhizoctonia root rot of sugar beet were recorded in two field trials in 2007 and 2008, and analysed using epidemiological modelling. Differences between partial biofumigation, involving the pulling up of mustard plants, and complete biofumigation, involving the crushing and incorporation of mustard residues into the soil, were compared with bare soil treatment. An epidemiological model was used that includes rates of transmission of primary and secondary infection, pre-emergence damping off, and expression of wilting symptoms (above-ground disease) due to infected roots (below-ground disease). The model indicated that biofumigation reduces the transmission of primary infections but affects secondary infections in a variable pattern between field trials. Likewise, the proportion of infected plants expressing wilting was significantly reduced, by 28%, in the partial and complete biofumigation treatments compared with bare soil in the trial of 2007 but not in 2008. It is suggested that the effects of biofumigation on secondary infection and the expression of disease are more variable than those on primary infection, and that this is probably due to an interplay between pathogen, antagonists, host, and environmental factors. These interactions may or may not offset the benefits afforded by a reduction in primary infection and account for the overall variable success of biofumigation to control disease.